The AIMS Long-term Monitoring Program (LTMP) is designed to detect changes in reef communities at a subregional scale. In this context, a subregion encompasses inshore, mid-shelf and outer shelf reefs across the continental shelf within one band of latitude (a sector).Reef surveys involve three approaches:1. broadscale manta tow surveys of crown-of-thorns starfish populations and reef-wide coral cover2. Intensive photographic surveys of stationary seafloor (benthic) organisms on fixed transects3. intensive visual counts of reef fish, juvenile corals, crown-of-thorns starfish, coral-eating snails and coral disease and bleaching.

In 6 sectors of the Great Barrier Reef (Cooktown/Lizard island, Cairns, Townsville, Whitsunday, Swain and Capricorn Bunker) 49 of the key manta tow reefs are designated 'core' survey reefs and are also surveyed using the scuba search technique. Where possible, three or more reefs in each sector have been selected in each of three positions across the continental shelf: inshore, mid-shelf and outer shelf. Results of scuba searches for juvenile Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. Observations have been obtained since October 1989 and are ongoing. Data includes counts of COTS and Drupella, coral feeding scars caused by COTS and Drupella, and the outbreaking status of COTS and Drupella. Also recorded are the percentage of bleached coral and the number of corals affected by disease. Diseases identified are: white syndrome, black band, skeletal eroding band and brown band. Any scar of unknown origin is also recorded. Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, dominant coral life form). To facilitate causes of coral mortality including juvenile and adult Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. To assess the amount of coral bleaching and disease. Bleaching is recorded as a percentage of the total hard coral cover: 0=absent, 0+ = individual colonies, -1= 1-5%, +1= 6-10%, 2=11-30%, 3=31-50%, 4 =51-75%, 5=76-100%

64 'key' reefs in 11 sectors of the Great Barrier Reef (Cape Grenville, Princess Charlotte Bay, Cooktown/Lizard Island, Cairns, Innisfail, Townsville, Cape Upstart, Whitsunday, Pompey Complex, Swain and Capricorn Bunker) are annually surveyed for crown-of-thorns starfish using the manta tow technique. An additional 117 reefs from the sectors (excluding the Whitsunday, Swain and Capricorn-Bunker sectors) are scheduled for survey every third year ('cycle' reefs). The cycle manta tow reefs take second priority if surveys are unable to be completed because of bad weather and limited ship time. Results of manta tow surveys around the perimeter of reefs assessing populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris. Historical data are held from a number of projects - P. Moran's post-doctoral work, CCEP scheme, COTSAC, COTSREC, LTMP. All data are stored in the Oracle database table RM_MANTA, and data from all but the first listed program are generally consistent and systematic. In the latest and ongoing program - the Long Term Monitoring Program (LTMP) - about 50 reefs throughout the Great Barrier Reef and NW Australia have been sampled. Observations started in January 1982 and are ongoing. For each two-minute manta tow the variables recorded are: Number and size of COTS; Percentage cover of live coral, dead coral, and soft coral; Visibility; Any other observations of note. The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions:(Wind strength; Cloud cover; Sea state; and Tide). Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, and dominant coral life form). To assess populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, on reefs. Coral Reef - Feeding Scar, Crown of Thorns Starfish - Diameter, Crown of Thorns Starfish - Outbreak Status, Percentage Cover, Count - Individuals, Turbidity Number and size of COTS. Size is recorded as follows: J = less than or equal to 5cm, early juvenile, <1 yr; A = 6-15cm Juvenile, 1-2 yrs; B = 15-25cm Sub-Adult, 2-3 yrs; C = >25cm Adult, >3 yrs). If no COTS are seen, then the column is left blank. When several size categories are seen, the category with the most numerous counts is recorded, and a note is made of the other size categories in the 'other' column. Percentage cover of live coral, dead coral, and soft coral. Categories are: 0 = 0%, 1- = 1-5%, 1+ = 5-10%, 2 = 10-30%, 3 = 30-50%, 4 = 50-75%, 5 = 75-100%. Presence of COTS feeding scars: absent (A: 0), present (P: 1-10) or common (C >10). The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions: Wind strength categories: 1 = 0-5 knots; 2 = 6-10 knots; 3 = 11-15 knots; 4 = 16-20 knots; 5 = 21-25 knots Cloud cover unit of measure is the okta. One okta = one eigth of the sky. Sea State. A modified Beaufort scale describes sea state: Calm = Mirror-like to small ripples; Slight = Small waves, some whitecaps; Moderate = Moderate waves, many whitecaps; Rough = Large waves 2-3 m, whitecaps everywhere, some spray Tide is recorded as low (1.5 hrs either side of Low water), high (1.5 hrs either side of High water), falling (between High and Low water) or rising (between Low and High water), determined from a Tide Table. Data have been used for the e-Atlas: http://e-atlas.org.au/content/large-scale-manta-tow-surveys-densities-crown-thorns-starfish-and-benthic-cover-aims-ltmp

64 'key' reefs in 11 sectors of the Great Barrier Reef (Cape Grenville, Princess Charlotte Bay, Cooktown/Lizard Island, Cairns, Innisfail, Townsville, Cape Upstart, Whitsunday, Pompey Complex, Swain and Capricorn Bunker) are annually surveyed for crown-of-thorns starfish using the manta tow technique. An additional 117 reefs from the sectors (excluding the Whitsunday, Swain and Capricorn-Bunker sectors) are scheduled for survey every third year ('cycle' reefs). The cycle manta tow reefs take second priority if surveys are unable to be completed because of bad weather and limited ship time. Results of manta tow surveys around the perimeter of reefs assessing populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris. Historical data are held from a number of projects - P. Moran's post-doctoral work, CCEP scheme, COTSAC, COTSREC, LTMP. All data are stored in the Oracle database table RM_MANTA, and data from all but the first listed program are generally consistent and systematic. In the latest and ongoing program - the Long Term Monitoring Program (LTMP) - about 50 reefs throughout the Great Barrier Reef and NW Australia have been sampled. Observations started in January 1982 and are ongoing. For each two-minute manta tow the variables recorded are: Number and size of COTS; Percentage cover of live coral, dead coral, and soft coral; Visibility; Any other observations of note. The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions:(Wind strength; Cloud cover; Sea state; and Tide). Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, and dominant coral life form). To assess populations of Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, on reefs. Coral Reef - Feeding Scar, Crown of Thorns Starfish - Diameter, Crown of Thorns Starfish - Outbreak Status, Percentage Cover, Count - Individuals, Turbidity Number and size of COTS. Size is recorded as follows: J = less than or equal to 5cm, early juvenile, <1 yr; A = 6-15cm Juvenile, 1-2 yrs; B = 15-25cm Sub-Adult, 2-3 yrs; C = >25cm Adult, >3 yrs). If no COTS are seen, then the column is left blank. When several size categories are seen, the category with the most numerous counts is recorded, and a note is made of the other size categories in the 'other' column. Percentage cover of live coral, dead coral, and soft coral. Categories are: 0 = 0%, 1- = 1-5%, 1+ = 5-10%, 2 = 10-30%, 3 = 30-50%, 4 = 50-75%, 5 = 75-100%. Presence of COTS feeding scars: absent (A: 0), present (P: 1-10) or common (C >10). The ambient variables recorded include, information about the survey (reef name, time, date, data collectors), and the weather conditions: Wind strength categories: 1 = 0-5 knots; 2 = 6-10 knots; 3 = 11-15 knots; 4 = 16-20 knots; 5 = 21-25 knots Cloud cover unit of measure is the okta. One okta = one eigth of the sky. Sea State. A modified Beaufort scale describes sea state: Calm = Mirror-like to small ripples; Slight = Small waves, some whitecaps; Moderate = Moderate waves, many whitecaps; Rough = Large waves 2-3 m, whitecaps everywhere, some spray Tide is recorded as low (1.5 hrs either side of Low water), high (1.5 hrs either side of High water), falling (between High and Low water) or rising (between Low and High water), determined from a Tide Table. Data have been used for the e-Atlas: http://e-atlas.org.au/content/large-scale-manta-tow-surveys-densities-crown-thorns-starfish-and-benthic-cover-aims-ltmp

The Australian Institute of Marine Science (AIMS) has been running coral reef monitoring programs since the 1980s, including both the Long-Term Monitoring Program (LTMP) and Marine Monitoring Program (MMP). These monitoring programs are designed to detect changes in coral reef communities at a sub-regional scale. Within this context, a subregion consists of inshore, mid-shelf, and outer shelf reefs across the continental shelf within one band of latitude (considered a sector). Data are modelled for presentation on the AIMS Reef Reporting Dashboard https://apps.aims.gov.au/reef-monitoring/reefs. The Reef Monitoring Reporting (MonRep) platform displays modelled data collected by AIMS' Long-Term Monitoring Program and Marine Monitoring Program at reef level, latitudinal Sector or Natural Resource Management (NRM)-region level in the Reef Monitoring Tool. How the data has been modelled for each graph is explained below for each data type. Benthic community cover Reef-level photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral, algae and soft corals) a model containing the population-level effects of year crossed with major taxonomic groups and the varying effects of transects nested within sites were fit to binomial photo point counts. NRM-region/Sector photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector and major benthic group (live hard coral, macroalgae and soft corals) a model containing the population-level effects of year and the varying effects of depth and transects nested within sites nested within reefs were fit to binomial photo point counts. Manta tow surveys Reef-level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows were fit against a beta distribution to percentage cover data. For NRM region//Sector level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows nested within reef were fit against a beta distribution to percentage cover data. Juvenile hard corals Reef-level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, a model containing the population-level effects of year and the varying effects of sites were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. NRM region/Sector level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, for each NRM region/Sector a model containing the population-level effects of year and the varying effects of sites nested within reefs were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. Reef fish Reef-level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites were fit against zero-inflated negative binomials. NRM region/Sector level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each NRM region/Sector and for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites nested

Monitoring has been carried out on inshore reefs since 2005. Benthic community monitoring program variables: Ongoing: percent cover of benthic organisms nominally to genus level resolution (hard corals, soft corals and macroalgae); densities of juvenile corals; prevalence of coral diseases; Ended (last sample): settlement of coral larvae to tiles(2012); numbers of genera; size distributions of coral colonies (2005); composition of benthic Foraminifera communities (2014, ongoing collection of samples in storage). Sediment sample variables: grain size fractions; nitrogen; organic, inorganic and total carbon (2014, grainsize samples in storage). Sediment samples 2015-2020 collected, in storage but no grainsize or chemical analysis undertaken. Geographic areas (note not all locations have all data in all years) relate to Natural Resource Management (NRM): Wet Tropics NRM, NQ Dry Tropics NRM, Mackay Whitsunday Isaac NRM, Fitzroy Basin NRM. Reef locations: Barren Island, Bedarra Island (started 2016), Daydream Island, Dent Island, Double Cone Island, Dunk Island, Fitzroy Island, Frankland Group, Geoffrey Bay, Havannah Island, High Island, Hook Island, Humpy & Halfway Island, King Reef (ended 2014), Lady Elliot Reef, Middle Island, Middle Reef (ended 2014), North Barnard Group, North Keppel Island, Orpheus Island, Pandora Reef, Peak Island (ended 2020), Pelican Island, Pelorus Island, Pine Island, Seaforth Island, Shute & Tancred Island, Snapper Island, Cape Tribulation fringing reefs (ended 2006). Data monitors the condition of coral community characteristics on inshore reefs of the Great Barrier Reef. This dataset is associated with another dataset on inshore water quality under Reef Plan MMP (see separate metadata record) The objective of the biological monitoring of nearshore reefs is to document trends in the benthic reef communities on selected nearshore reefs. These changes may be due to acute disturbances such as cyclonic winds, bleaching and crown-of-thorns starfish as well as those related to land runoff (e.g. floods), which disrupt processes of recovery such as recruitment and growth. These data are collected in conjunction with another dataset: Inshore Water Quality as part of the Reef Rescue Marine Monitoring Program. Benthic Cover from pre 2007 was estimated from video frames, from 2007 on from digital photos Sampling of coral size classes changed from 5 by 10m long transects at each site and depth and all coral sizes in 2005 and 2006 to only sizes 0-2cm, 2-5cm and 5-10cm in 5 by 20m long transects from 2007 to 2017, and then only 0-2cm and 2-5cm size classes from 2018 on. Sampling design: coral community attributes are monitored at both 2m and 5m depths below lowest astronomical tide at each of two sites on each reef. Within site and depth combinations are five 20m transects marked with steel pickets at the beginning and steel rod at the middle and each end. Markers are maintained through time. Compass directions are maintained for entire site. Frequency of sampling has varied over the duration of this program. All reefs were sampled in 2005 and 2006, from 2007 to 2014 a set of 14 core reefs, at which water-quality was also monitored, and Snapper Island, were surveyed annually with the remainder scheduled for sampling on a biennial cycle. Opportunistic sampling over this period infilled with unscheduled samples after some severe disturbance events. From 2015 to 2018 reefs were scheduled for biennial sampling with half of the reefs in each region sampled in alternate years, contingency sampling was included to resample unscheduled reefs in the event of a disturbance. In 2019 all reefs, other than Peak were sampled and the sample of all reefs scheduled from 2020. Benthic cover is estimated from digital photos taken at 50cm intervals along the upslope side of the marked transects. Incidence of coral mortality and disease are counted within 2m wide belts centred on the marked transects. Small size-class corals are counted

70 selected reefs throughout the Great Barrier Reef (GBR) are sampled in the AIMS Long-term Monitoring Project (LTMP). Underwater visual census is used to survey reef fishes on fixed transects (3 sites per reef, 5 x 50 m transects per site). The abundance and length of all diurnally active, non-cryptic fishes are recorded. A full list of species observed each year can be obtained on request. The overarching goal of LTMP fish surveys are to detect changes in reef fish communities over time at a regional scale, but also to examine the effectiveness of Marine Protected Areas. All fish species counted are largely non-cryptic, easily identified underwater and include both commercial and non-commercial taxa. Because surveys span the annual recruitment season, 0+ individuals are excluded from counts: these are distinguished from adults by their small size and often distinctive colouration. Abundance data for each fish species is subsequently summed over the five transects at each site on each reef to provide reasonable sample sizes for analysis and interpretation. Updated results of surveys can be found at: https://apps.aims.gov.au/reef-monitoring/reefs A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://www.iobis.org/explore/#/dataset/3936). Data have been used for the e-Atlas: http://eatlas.org.au/data/uuid/05bde62a-70ec-407b-b999-30cf369498af

The coral and communities at the AIMS Long Term Monitoring (LTM) sites at Scott Reef, Seringapatam and Rowley Shoals were re-surveyed, following periodic surveys since 1994. In addition to the Proposed Field Program, the following work was completed: Benthic LTM surveys at three additional sites at Scott Reef. Coral species diversity surveys at four additional sites at Scott Reef. Benthic LTM surveys of coral communities at 13 sites in the deep lagoon (20-60m) at South Reef using ROV. Colony size-frequency surveys at six sites at Scott Reef. Genetic samples of surviving Seriatopora hystrix from 7 sites at Scott Reef. Additional temperature loggers and current metres deployed at Rowley Shoals. Video and photographic documentation of the Rowley Shoals, in water and from air using drones This project is a co-investment between Woodside Energy Ltd (WEL) and AIMS, in order to build scientific knowledge at Scott Reef, Seringapatam and Rowley Shoals and was undertaken between 4th – 25th November 2017.